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(-) Description

Title :  CRYSTAL STRUCTURE OF H334R HDAC8 IN COMPLEX WITH M344
 
Authors :  C. Decroos, C. B. Bowman, J. -A. S. Moser, K. E. Christianson, M. A. Deard D. W. Christianson
Date :  02 May 14  (Deposition) - 06 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Metalloenzyme, Hydrolase, Histone Deacetylase, Enzyme Inhibitor Complex, Cornelia De Lange Syndrome, Arginase/Deacetylase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Decroos, C. M. Bowman, J. A. Moser, K. E. Christianson, M. A. Deardorff, D. W. Christianson
Compromised Structure And Function Of Hdac8 Mutants Identified In Cornelia De Lange Syndrome Spectrum Disorders
Acs Chem. Biol. V. 9 2157 2014
PubMed-ID: 25075551  |  Reference-DOI: 10.1021/CB5003762

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    Chains: A
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHD2-XA-HIS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HDAC8, HDACL1, CDA07
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GOL3Ligand/IonGLYCEROL
3K2Ligand/IonPOTASSIUM ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GOL3Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1B3N2Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GOL6Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:100 , ASP A:101 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , PRO A:273 , MET A:274 , TYR A:306 , ZN A:502 , HOH A:702BINDING SITE FOR RESIDUE B3N A 501
2AC2SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , B3N A:501BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200BINDING SITE FOR RESIDUE K A 503
4AC4SOFTWAREPHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:604 , HOH A:608BINDING SITE FOR RESIDUE K A 504
5AC5SOFTWAREGLN A:236 , SER A:351 , CYS A:352 , ARG A:353BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWARELYS A:289 , TYR A:317 , VAL A:321 , GLY A:324 , LYS A:325 , THR A:326 , HOH A:617BINDING SITE FOR RESIDUE GOL A 506
7AC7SOFTWARESER A:215 , ASP A:216 , VAL A:217 , GLY A:218 , ARG A:223BINDING SITE FOR RESIDUE GOL A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QA4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:208 -Pro A:209
2Gly A:341 -Pro A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QA4)

(-) Exons   (0, 0)

(no "Exon" information available for 4QA4)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh.....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qa4 A  13 SLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDREFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVI 378
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QA4)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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  4qa4
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  3.5.1.98
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HDAC8_HUMAN | Q9BY41: 1t64 1t67 1t69 1vkg 1w22 2v5w 2v5x 3ew8 3ewf 3ezp 3ezt 3f06 3f07 3f0r 3mz3 3mz4 3mz6 3mz7 3rqd 3sff 3sfh 4qa0 4qa1 4qa2 4qa3 4qa5 4qa6 4qa7 4rn0 4rn1 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5dc8 5fcw 5ths 5tht 5thu 5thv

(-) Related Entries Specified in the PDB File

4qa0 4qa1 4qa2 4qa3 4qa5 4qa6 4qa7